11:00 A – 7:00 P
Snail
- Rewrite fxn_Figs_y_v_snail to render only figures indicated in list Plotnames and show them in the indicated figure:
ff = strfind(Plotnames,'box_CoVratio'); ff = find(1 - cellfun(@isempty, ff)); if ~isempty(ff) figure(Plotnumbers(ff)); clf; ... end
- This facilitates use of export_fig to render figure. .eps at least perserves vector format even if transparencies are used, though the transparencies are lost and have to be reset in Illustrator.
- Haven’t tried out export svg code yet.
- Monet now has pdftops and ghostscript installed for use with export_fig command.
- Script_y_v_sna currently configured to produce the whole range of ageclasses for spatial figures for MP05 data. (including all new data).
Coding
- Updated ReadDax
- now specifies arbitrary start and end frames
- imageDimension was unused / non-functional and I removed it
- start and end frames makes allFrames redundant. (just leave end frames empty for all frames and make = 1 for first frame only). This now automatically reparses into start and end frame input (preserves backwards compatibility).
- What is ‘quiet’ (unused variable)?
- GPU processing
- work through sample GPU code to get running on my data. visualize raw data and dot-finding results — tune input parameters for a good match.
- GPU single-emitter fitting looks functional and robust.
- Object-oriented matlab program (everything is part of a ‘class’ structure).
- Discuss with Jeff organization and logic of object-oriented programming. Jeff thinks this is a good idea, matlab moving more support in this direction.
- I think most matlab programmers are used to non-object oriented approach, this is a little harder to get used to. Currently I’m going to try to wrap these into function based matlab codes.
- GPU multi-emitter fitting
- doesn’t like extra bright spots.
- scaling to photon number seems to do pretty well at finding the other dots though.
- Multifitter >5 tends to crash during analysis (can always make input size smaller, but does require restart of Matlab).
- writing matlab wrappers GPUmultifitDax.m and GPUmultifit to run the multifitter code
- # writing matlab wrapper GPUfit3D to wrap the 3D single-emitter code
- Programming goal planning with Jeff
- Wrote to Will and Fang about source code.
Probe Making
- precipitated and re-suspended digests on En oligoPAINT probe